Investigation of the composition, function and evolutionary dynamics of microRNAs in fish genomes using RNA-Seq and reverse genetics

• Grant number: 12/15589-7
• Support Opportunities: Regular Research Grants
• Duration: November 01, 2012 - June 30, 2015
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Danillo Pinhal
• Grantee: Danillo Pinhal
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Associated researchers: César Martins ; Ney Lemke

Abstract

MicroRNAs (miRNAs) are small endogenous RNAs of ~22 nucleotides that regulate cellular transcriptome by partial or complete pairing with complementary sequences of its target messenger RNAs (mRNA), thus controlling the protein production. In vertebrates, owing to the observed association between miRNA abundance and diversity with increased complexity of the taxonomic group, miRNAs become important elements both for understanding the evolution of genes, transcripts and regulatory mechanisms, as well as phylogenetic markers in comparative genomics. In fish, the largest group of living vertebrates, among the ~ 30,000 known species, only a small fraction was investigated regarding miRNAs composition and expression. Furthermore, the vast majority of miRNAs found in vertebrate genomes needs to be functionally characterized. In the present project we propose a two-fold strategy for studying miRNAs using as biological models the fish species zebrafish (Danio rerio) and nile tilapia (Oreochromis niloticus) with complete genome sequenced. The first step involves the use of next generation sequencing (RNA-seq) combined with comparative genome analysis to determine the overall composition and investigate the genomic organization, diversity and evolutionary dynamics of miRNA families. In the second step, we propose the implementation of reverse genetics experiments for functional analysis of miRNAs, using the data previously gathered by RNA-seq. In the functional experiments, synthetic molecules that mimic or block the action of miRNAs will be microinjected in embryos, allowing for the association between the altered gene and the respective phenotype produced. From these experiments, intended for the integration of structural and functional genomic data, it will be feasible to identify combinations of miRNAs and target mRNAs, as well as link them to the evolution of clades and regulation of specific biological processes. (AU)

Scientific publications

(8)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

NACHTIGALL, PEDRO GABRIEL; DIAS, MARCOS CORREA; PINHAL, DANILLO. Evolution and genomic organization of muscle microRNAs in fish genomes. BMC Evolutionary Biology, v. 14, SEP 25 2014. (12/15589-7)

HERKENHOFF, M. E.; RIBEIRO, A. O.; COSTA, J. M.; OLIVEIRA, A. C.; DIAS, M. A. D.; REIS NETO, R. V.; HILSDORF, A. W. S.; PINHAL, D.. Expression profiles of growth-related genes in two Nile tilapia strains and their crossbred provide insights into introgressive breeding effects. ANIMAL GENETICS, v. 51, n. 4, MAY 2020. (14/03062-0, 12/15589-7)

HERKENHOFF, MARCOS E.; OLIVEIRA, ARTHUR C.; NACHTIGALL, PEDRO G.; COSTA, JULIANA M.; CAMPOS, VINICIUS F.; HILSDORF, ALEXANDRE W. S.; PINHAL, DANILLO. Fishing Into the MicroRNA Transcriptome. FRONTIERS IN GENETICS, v. 9, MAR 19 2018. (14/03062-0, 13/06864-7, 12/15589-7)

PINHAL, DANILLO; BOVOLENTA, LUIZ A.; MOXON, SIMON; OLIVEIRA, ARTHUR C.; NACHTIGALL, PEDRO G.; ACENCIO, MARCIO L.; PATTON, JAMES G.; HILSDORF, ALEXANDRE W. S.; LEMKE, NEY; MARTINS, CESAR. Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development. SCIENTIFIC REPORTS, v. 8, MAY 29 2018. (12/13450-1, 12/15589-7, 15/16661-1, 15/19176-7, 11/06465-0, 13/06864-7)

NACHTIGALL, PEDRO G.; DIAS, MARCOS C.; CARVALHO, ROBSON F.; MARTINS, CESAR; PINHAL, DANILLO. MicroRNA-499 Expression Distinctively Correlates to Target Genes sox6 and rod1 Profiles to Resolve the Skeletal Muscle Phenotype in Nile Tilapia. PLoS One, v. 10, n. 3, MAR 20 2015. (11/06465-0, 13/06864-7, 12/15589-7)

OLIVEIRA, UR C.; BOVOLENTA, LUIZ A.; ALVES, LUCAS; FIGUEIREDO, LUCAS; RIBEIRO, AMANDA O.; CAMPOS, VINICIUS E.; LEMKE, NEY; PINHAL, DANILLO. Understanding the Modus Operandi of MicroRNA Regulatory Clusters. CELLS, v. 8, n. 9, SEP 2019. (18/05484-0, 18/26409-6, 12/13450-1, 12/15589-7, 15/19176-7, 17/17510-2)

BOVOLENTA, LUIZ AUGUSTO; PINHAL, DANILLO; ACENCIO, MARCIO LUIS; DE OLIVEIRA, ARTHUR CASULLI; MOXON, SIMON; MARTINS, CESAR; LEMKE, NEY. miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data. CELLS, v. 9, n. 8, AUG 2020. (10/20684-3, 12/13450-1, 12/15589-7, 14/08420-1, 15/19176-7, 11/06465-0, 13/03644-6)

NACHTIGALL, PEDRO G.; BOVOLENTA, LUIZ A.; PATTON, JAMES G.; FROMM, BASTIAN; LEMKE, NEY; PINHAL, DANILLO. A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks. BMC Genomics, v. 22, n. 1, MAR 4 2021. (13/06864-7, 12/15589-7)